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Single-cell multiomics reveals the oscillatory dynamics of RNA metabolism and chromatin accessibility during the cell cycle

GSE300730 Mus musculus Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing 4 samples Submitted 2025/06/25 Platform GPL30172
Summary
The cell cycle is a tightly regulated process that requires precise temporal expression of hundreds of cell cycle-dependent genes. However, the genome-wide dynamics of mRNA metabolism throughout the cell cycle remain uncharacterized. Here, we combined single-cell multiome sequencing, biophysical modeling, and deep learning to quantify rates of mRNA transcription, splicing, nuclear export, and degradation. Our approach revealed that both transcriptional and post-transcriptional processes exhibit distinct oscillatory waves at specific cell cycle phases, with post-transcriptional regulation playing a prominent role in shaping mRNA accumulation. We also observed dynamic changes in chromatin accessibility and transcription factor binding footprints, identifying key regulators underlying the oscillatory dynamics of mRNA. Taken together, our approach uncovered a high-resolution map of RNA metabolism dynamics and chromatin accessibility, offering new insights into the temporal control of gene expression in proliferating cells.
Published in
Single-cell multiomics reveals the oscillatory dynamics of mRNA metabolism and chromatin accessibility during the cell cycle
Nariya MK, Santiago-Algarra D, Tassy O et al. · Cell reports 2025 · PMID 40751912 · doi:10.1016/j.celrep.2025.116089
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Direct links to NCBI, no account and no request form: the whole study as GSE300730_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 4 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA1281951 and SRA study SRP594493. Searching any of these in the dataset finder brings you back here.

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